Set amidst the ancient ruins of Sarnath, Mulagandha Kuti Vihar has a distinct architecture which is very different from that of the other temples. This is because the temple is a more recent addition, constructed by Maha Bodhi society in 1931. The temple is very impressive boasting detailed design and patterns in its interiors as also beautiful murals and frescos made by Kosetsu Nosu, one of the foremost painters of Japan. While murals are found in the interiors, the exterior is decorated with murals.

There is also a huge bronze bell at the entrance of the vihar that was gifted by the royal family of Japan. The sanctum houses a magnificent life-size golden statue of the Buddha. The temple also has a Bodhi tree that has been transplanted from a sapling brought from a tree in Sri Lanka. The tree in Sri Lanka originated from the real tree under which Buddha attained enlightenment in Bodh Gaya some 2500 years ago.